PB1799: KMT2A-REARRANGED PEDIATRIC ACUTE MYELOID LEUKEMIA
Authors: E. Zerkalenkova, S. Lebedeva, A. Borkovskaia, Y. Menchits, M. Gaskova, A. Itov, E. Matveev, M. Kazanov, Y. Olshanskaya
Journal: HemaSphere (2022)

Background: Histone-lysine N-methyltransferase 2A gene rearrangements (KMT2A-r) are common genetic events in acute leukemia. They demonstrate great molecular heterogeneity with more than 90 partner genes and multiple KMT2A breakpoints involved. These characteristics challenge both the initial molecular diagnostics and MRD monitoring in ALs with KMT2A-r. On the other hand, the profile of accompanying mutations is relatively quiet in this type of leukemia due to strong oncogenic potential of KMT2A rearrangement itself. Aims: Our recent study aims to characterize KMT2A-rearranged acute myeloid leukemia in children in Russian Federation both in terms of partner genes involved and in accompanying mutations study. Methods: A cohort of 313 KMT2A-positive AMLs in children aged 4 days to 18 y.o. (median 2 y.o.; 162 boys and 151 girls) was analyzed using G-banded karyotyping and FISH together with real-time and nested RT-PCR. Transcripts were Sanger sequenced. Patients with rare or unknown translocations were subjected to long-distance inverse PCR (LDI-PCR), anchored multiplex PCR (ArcherDX, CO, USA) or custom targeted KMT2A enrichment panel (Illumina, CA, USA; Meyer et al., 2019). Additional events were characterized by fragment analysis, Sanger sequencing and NGS (Qiagen Myeloid Neoplasms panel, Hilden, Germany) in 113 cases included in Russian AML registration study and AML-MRD-2018 local treatment protocol. Results: The incidence of KMT2A-rs was the highest in children under 2 y.o. inclusive (n=120, 38%) and goes down with age. A total of 26 different KMT2A-rs were found in 296 patients (94.6%). The prevailing translocations were as follows: t(9;11)(p21;q23.3)/KMT2A-MLLT3 (n=129, 41.21%), t(10;11)(p12;q23.3)/KMT2A-MLL10 (n=71, 22.68%), t(11;19)(q23.3;p13.1)/KMT2A-ELL (n=24, 7.67%), t(6;11)(q27;q23.3)/KMT2A-AFDN (n=15, 4.79%), t(11;19)(q23.3;p13.3)/KMT2A-MLLT1 (n=13, 4.15%). Other translocation partners were much rarer, for 15 partner genes only single cases were found. Three novel KMT2A-rs were identified, namely t(11;16)(q23;q23.3)/KMT2A-USP10, t(X;11)(q22.1;q23.3)/KMT2A-BTK and t(X;11)(q26.3;q23.3)/KMT2A-CT45A. KMT2A breakpoint location was analyzed in 274 patients (87,54%). It was found in introns 7 to 12, which is narrower than in ALL, and was most often situated in introns 9 (n=131, 47.81%) and 10 (89 cases, 32.48%) as numbered by Meyer et al. [Meyer et al., 2006]. Intron 9 was also predominant in rearrangements with all but MLLT1 frequent translocation partners and most rare translocation partners. KMT2A break outside the main cluster was found in intron 7 on 4 cases of KMT2A-MLL10. The achieved data on KMT2A translocation partners and breakpoint locations was used for subsequent patient-specific MRD monitoring. The molecular profile of myeloid neoplasms-associated gene was studied in 113 samples. One to 9 additional pathogenic somatic events (median 4) with variant allele frequency above 1% were found in the studied cohort with most of them being subclonal (VAF<10%). Only 62 samples contained additional mutations with VAF greater above 10%. Among them NRAS (n=11 of 62, 17.74%), KRAS (n= 8, 12,90%) and PTEN11 (4, 6,45%) were prevalent. Accompanying mutations did not exhibit translocation partner preference. Summary/Conclusion: Molecular profiling of KMT2A-rearranged AML in Russian Federation reveals the highest incidence of KMT2A-MLLT3 fusion gene and KMT2A intron 9 involvement. Our data also confirms the relatively quiet landscape of accompanying mutations in KMT2A-rearranged AML with RAS pathway most frequently involved.